Dear FreeSurfer experts,
My question is in the title. I'm working on Alzheimer case where most of the cases have large ventricles. Is it better in general use to apply -bigventricles option on all subjects (for homogeneous calculus or something like that...) or to distinct subtle cases of patients with not so big ventricles ?
Thanks in advance for helping !
Best regards,
Matthie
Hi Matthie
do you find that it doesn't work well without bigventricles? You just want to be sure that you process your data in the same way so there is no bias in the results. We have found that most early AD cases work fine without needing special flags. It's more for late stage AD or hydrocephalus and such.
cheers Bruce
On Thu, 3 Dec 2015, Matthieu Vanhoutte wrote:
Dear FreeSurfer experts,
My question is in the title. I'm working on Alzheimer case where most of the cases have large ventricles. Is it better in general use to apply -bigventricles option on all subjects (for homogeneous calculus or something like that...) or to distinct subtle cases of patients with not so big ventricles ?
Thanks in advance for helping !
Best regards,
Matthie
Hi Bruce,
Exactly I want to be sure that I process my data in the same way, so not introduce bias with partially use of -bigventricles option.
1) I tried the recon-all process on AD patient with big ventricles and atrophy with and without the -bigventricles option. I am not pretty sure of which process is the best in terms of segmentation according the aseg.mgz ? (I'll send you T1 and aseg.mgz for the two process) 2) Considering cortical atrophy, a lot of gray matter hasn't been taken account in the cortex segmentation. Is there an automatic way to improve the cortical segmentation in case of visible atrophy ?
Best regards, Matthieu
2015-12-03 18:03 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Matthie
do you find that it doesn't work well without bigventricles? You just want to be sure that you process your data in the same way so there is no bias in the results. We have found that most early AD cases work fine without needing special flags. It's more for late stage AD or hydrocephalus and such.
cheers Bruce
On Thu, 3 Dec 2015, Matthieu Vanhoutte wrote:
Dear FreeSurfer experts,
My question is in the title. I'm working on Alzheimer case where most of
the cases have large
ventricles. Is it better in general use to apply -bigventricles option
on all subjects (for
homogeneous calculus or something like that...) or to distinct subtle
cases of patients with not so
big ventricles ?
Thanks in advance for helping !
Best regards,
Matthie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Bruce,
I got no answer to my questions below with files provided thanks to FileDrop.
Could you tell me if you received these questions and associated files ?
Thanks in advance !
Best regards, Matthieu
2015-12-04 15:17 GMT+01:00 Matthieu Vanhoutte matthieuvanhoutte@gmail.com:
Hi Bruce,
Exactly I want to be sure that I process my data in the same way, so not introduce bias with partially use of -bigventricles option.
- I tried the recon-all process on AD patient with big ventricles and
atrophy with and without the -bigventricles option. I am not pretty sure of which process is the best in terms of segmentation according the aseg.mgz ? (I'll send you T1 and aseg.mgz for the two process) 2) Considering cortical atrophy, a lot of gray matter hasn't been taken account in the cortex segmentation. Is there an automatic way to improve the cortical segmentation in case of visible atrophy ?
Best regards, Matthieu
2015-12-03 18:03 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Matthie
do you find that it doesn't work well without bigventricles? You just want to be sure that you process your data in the same way so there is no bias in the results. We have found that most early AD cases work fine without needing special flags. It's more for late stage AD or hydrocephalus and such.
cheers Bruce
On Thu, 3 Dec 2015, Matthieu Vanhoutte wrote:
Dear FreeSurfer experts,
My question is in the title. I'm working on Alzheimer case where most
of the cases have large
ventricles. Is it better in general use to apply -bigventricles option
on all subjects (for
homogeneous calculus or something like that...) or to distinct subtle
cases of patients with not so
big ventricles ?
Thanks in advance for helping !
Best regards,
Matthie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Matthieu Vanhoutte